First of the Savage Skies series.
After running afoul of timberwolves in the Everfree Forest, Fluttershy is saved by a mysterious young colt with a most unusual and disturbing feature. Realizing that he is alone, without anyone else to care for him, Fluttershy realizes that she must try to bring this lonely foal out of the forest and give him a life of love and friendship. The problem is that this colt's...unique qualities have made him more than a few enemies, including some who are closer to home than Fluttershy realizes.

Now with a sequel: The Promise of a New Day.
Now with a TV Tropes page.

Following the events of the movie, Tempest Shadow accepts responsibility for her actions and attempts to atone for her actions while serving under the Storm King.

Author's Note:

Chapters 11-15 were written at Canterlot KC 2017 in Kansas City, MO

Chapters 59-61 were written at CONglomeration 2018 in Louisville, KY

Edited by SuperPinkBrony12

After a mistaken identity case, Fluttershy is wrongly accused of a murder attempt on one of the High Blood houses, and sentenced to twenty years of incarceration in the Brokenfang Maximum Security Prison, where the most dangerous and unpredictable Krussian criminals are sent. As her friends do what they can to prove her innocence and secure her release, Fluttershy must learn to survive in the hostile environment of Brokenfang, making both new friends and enemies, as well as to learn that not everypony is what it seems…

It was just another day in school for Fluttershy in Ponyville High. Conflict is brewing between two races, The Humans and The Trans-mutants, tensions are high, and prejudice to one another is rising higher than before. To make matters more tense, some of the Trans-mutants are being allowed to walk among them as well as attending the same schools. Fluttershy will cross boundaries that few would dare cross.....Making friends with one.
(A Humanized crossover fan fiction of Godzilla and MLP FIM. If you are familiar with "The Arrogance of Man" (http://www.fimfiction.net/story/220838/the-arrogance-of-man), then be aware that this is an alternate universe for the story). Sex tag is mostly for dialogue that may be deemed dirty at certain points, and intimacy. No sex scenes, keep this in mind. Cover art is by me, and props goes to Moongaze14 and ThePMB-Brony for proofreading this story. Thanks again guys!

Breaking the Walls Arc: In a world of humans and mutants, Fluttershy befriends a boy, Gojira Takeshi Jr, who has a gruff and pessimistic attitude, with a reputation to boot. Sometimes, it takes kindness to uncover what's beneath the surface. (Chapter 1-15)

Sins of the Father Arc: With his father back in his life, Junior finds himself caught up in situations that turn his entire world upside down. In comes new friends, and new revelations. From the shadows, enemies plot to bring chaos. And somehow, the Takeshi lineage is at the center of it. (Chapter 16-72).